# HG changeset patch
# User devteam
# Date 1450481829 18000
# Node ID 87f239da61af5023f5431fb46d232014d9d1f9e6
# Parent  8f755957b6a114821857a7ed4845481907c6c2d6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_cufflinks_2_2_1 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6

diff -r 8f755957b6a1 -r 87f239da61af tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 26 13:37:59 2014 -0500
+++ b/tool_dependencies.xml	Fri Dec 18 18:37:09 2015 -0500
@@ -3,15 +3,15 @@
     <package name="cufflinks" version="2.2.1">
         <install version="1.0">
             <actions_group>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz</action>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
-                <actions os="darwin" architecture="x86_64">
-                    <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz</action>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
@@ -19,23 +19,23 @@
                 </actions>
                 <actions>
                     <package name="boost" version="1.53.0">
-                        <repository changeset_revision="7cc7949148d5" name="package_boost_1_53" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"  prior_installation_required="True" />
+                        <repository changeset_revision="a534981960ca" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="samtools" version="0.1.18">
-                        <repository changeset_revision="c0f72bdba484"  name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu/"  prior_installation_required="True" />
+                        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="eigen" version="3.2.0">
-                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu/"  prior_installation_required="True" />
+                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
-                    <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz</action>
+                    <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz</action>
                     <action type="set_environment_for_install">
-                        <repository changeset_revision="7cc7949148d5" name="package_boost_1_53" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"  prior_installation_required="True">
+                        <repository changeset_revision="a534981960ca" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="boost" version="1.53.0" />
                         </repository>
-                        <repository changeset_revision="c0f72bdba484"  name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu/"  prior_installation_required="True">
+                        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="samtools" version="0.1.18" />
                         </repository>
-                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu/"  prior_installation_required="True">
+                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="eigen" version="3.2.0" />
                         </repository>
                     </action>
@@ -43,10 +43,10 @@
                     <action type="shell_command">make &amp;&amp; make install</action>
                 </actions>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions_group>
         </install>
-        <readme></readme>
+        <readme />
     </package>
 </tool_dependency>